If you have a datatable column condition like this...
"columns": [
{ "data": "Name" },
{
"data": null,
"sortable": false,
"searchable": false,
"render": function render(data, type, row, meta) {
var output = "<a class=\"action-view btn btn-xs btn-outline-secondary\" title=\"View\" href=\"/View/" + row.id + "\"><span class=\"bx bx-edit-alt\"></span></a>";
return output;
}
}]
Search Builder column dropdown will still show the item

I looked at source code, and I could not find (yet) the spot where you are populating it